Merge branch 'master' into rr

public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -97,7 +97,6 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         if (!( walker instanceof TreeReducible ))
             throw new IllegalArgumentException("The GATK can currently run in parallel only with TreeReducible walkers");
 
-        traversalEngine.startTimers();
         ReduceTree reduceTree = new ReduceTree(this);
         initializeWalker(walker);
 

public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -44,7 +44,6 @@ public class LinearMicroScheduler extends MicroScheduler {
      * @param shardStrategy A strategy for sharding the data.
      */
     public Object execute(Walker walker, ShardStrategy shardStrategy) {
-        traversalEngine.startTimers();
         walker.initialize();
         Accumulator accumulator = Accumulator.create(engine,walker);
 
@@ -54,6 +53,7 @@ public class LinearMicroScheduler extends MicroScheduler {
             if ( done || shard == null ) // we ran out of shards that aren't owned
                 break;
 
+            traversalEngine.startTimersIfNecessary();
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
                 LocusWalker lWalker = (LocusWalker)walker;
                 WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleMetadata());

public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -57,6 +57,7 @@ public class ShardTraverser implements Callable {
 
     public Object call() {
         try {
+            traversalEngine.startTimersIfNecessary();
             long startTime = System.currentTimeMillis();
 
             Object accumulator = walker.reduceInit();

public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -115,7 +115,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     LinkedList<ProcessingHistory> history = new LinkedList<ProcessingHistory>();
 
     /** We use the SimpleTimer to time our run */
-    private SimpleTimer timer = new SimpleTimer("Traversal");
+    private SimpleTimer timer = null;
 
     // How long can we go without printing some progress info?
     private static final int PRINT_PROGRESS_CHECK_FREQUENCY_IN_CYCLES = 1000;
@@ -209,11 +209,16 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
         }
     }
     /**
-     * Should be called to indicate that we're going to process records and the timer should start ticking
+     * Should be called to indicate that we're going to process records and the timer should start ticking.  This
+     * function should be called right before any traversal work is done, to avoid counting setup costs in the
+     * processing costs and inflating the estimated runtime.
      */
-    public void startTimers() {
+    public void startTimersIfNecessary() {
-        timer.start();
+        if ( timer == null ) {
-        lastProgressPrintTime = timer.currentTime();
+            timer = new SimpleTimer("Traversal");
+            timer.start();
+            lastProgressPrintTime = timer.currentTime();
+        }
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -15,6 +15,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.JexlExpression;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
@@ -24,6 +25,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -224,12 +226,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
         }
         sampleNamesForStratification.add(ALL_SAMPLE_NAME);
 
-        // Initialize select expressions
-        for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
-            SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
-            jexlExpressions.add(sjexl);
-        }
-
         // Add select expressions for anything in the tranches file
         if ( TRANCHE_FILENAME != null ) {
             // we are going to build a few select names automatically from the tranches file
@@ -240,16 +236,27 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
             }
         }
 
+        // Initialize select expressions
+        for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
+            SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
+            jexlExpressions.add(sjexl);
+        }
+
         // Initialize the set of stratifications and evaluations to use
         stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
         Set<Class<? extends VariantEvaluator>> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
+        boolean usingJEXL = false;
         for ( VariantStratifier vs : getStratificationObjects() ) {
             if ( vs.getClass().getSimpleName().equals("Filter") )
                 byFilterIsEnabled = true;
             else if ( vs.getClass().getSimpleName().equals("Sample") )
                 perSampleIsEnabled = true;
+            usingJEXL = usingJEXL || vs.getClass().equals(JexlExpression.class);
         }
 
+        if ( TRANCHE_FILENAME != null && ! usingJEXL )
+            throw new UserException.BadArgumentValue("tf", "Requires the JexlExpression ST to enabled");
+
         // Initialize the evaluation contexts
         evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);